Trinucleotide mrna cap analogs

ABSTRACT

What is described is a trinucleotide cap analog comprising m 7 G(5′)p 3 -N 1 pN 2  for increased efficiency of in vitro transcription of m7G(5′)p 3 -RNA, wherein m 7 G is N 7 -methylguanosine or analog, (5′)p 3  is a 5′,5′-triphosphate bridge, and N 1  or N 2  or both ribonucleotide analogs linked to each other by a phosphate, p, and wherein the trinucleotide cap analog increases the efficiency of in vitro transcription.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/788,742, filed Oct. 19, 2017, which claims the benefit of U.S.Provisional Application No. 62/410,325, filed Oct. 19, 2016, each ofwhich is incorporated by reference herein in its entirety.

TECHNICAL FIELD

The description herein is directed to trinucleotide cap analogs forimproved in vitro mRNA synthesis and translation of m⁷G(5′)p₃-RNA.

BACKGROUND

Eukaryotic mRNAs have a cap structure at their 5′-termini. The capconsists of 7-methyl guanosine (m⁷G) and a triphosphate bridge, ppp(p₃), linking the 5′OH of m⁷G to the 5′OH of the 5′-terminal nucleotide,N, denoted m⁷G(5′)pppN (m⁷G(5′)p₃N). In eukaryotic cells, the capstructure participates in assembly of the translation initiation complexby binding eukaryotic translation initiation factor 4E (eIF-4E).

Although m⁷G(5′)p₃ can be used to initiate transcription with T7 or SP6DNA-dependent RNA polymerase in vitro, it has the disadvantage of havingto compete with guanine nucleotide (G) as the initiating nucleophile fortranscriptional elongation. As a result of this competition, less thanhalf of mRNA produced in vitro have a cap structure at their 5′ termini.

Dinucleotide m⁷G(5′)p₃(5′)G, in which a guanine nucleotide (G) is linkedvia its 5′OH to the triphosphate bridge, has been used as an initiatorof transcription. This dinucleotide has the disadvantage that the 3′-OHof either the m⁷G or G moiety serves as the initiating nucleophile fortranscriptional elongation that results in synthesis of two isomericRNAs of the form m⁷G(5′)p₃G(pN)_(n) and G(5′)p₃7G(pN)_(n), with onethird to one half of the caps oriented in the reverse direction,depending upon the ionic conditions of the transcription reaction.Further improvement of the orientation of the cap during in vitrotranscription is possible using cap analogues that replace the 3′-OHgroup with hydrogen or —OCH₃ (U.S. Pat. No. 7,074,596; Kore, 2006,Nucleotides, Nucleotides, and Nucleic Acids, 25: 307-14, and Kore, 2006,Nucleotides, Nucleotides, and Nucleic Acids, 25: 337-40).

Dinucleotide GG cap analogs m⁷G(5′)p₃G and 3′-OMe-m⁷G(5′)p₃G (ARCA) aresold commercially by TriLink BioTechnology, MilliporeSigma, ThermoFisherScientific, and New England BioLabs Inc. 3′-OMe-m⁷G(5′)p₃G (ARCA) isincorporated during transcription without reversal to G(5′)p₃ m⁷G.

Trinucleotide cap analogs were disclosed by Ishikawa, 2009, Nucleic AcidSymp. Ser., 53:129-30. These are as follows:

-   -   m⁷G(5′)p₃ApG, corresponding to the terminal trinucleotide of        plant RNA;    -   m⁷G(5′)p₃AmpG (Am is adenine with a 2′OMe-ribose), corresponding        to the terminal trinucleotide of animal RNA;    -   m⁷G(5′)p₃m⁶AmpG (m⁶A is N⁶-methyladenine), corresponding to the        terminal trinucleotide of mammal RNA; and    -   m⁷G(5′)p₃m⁶ApG, an unnatural trinucleotide.        Ishikawa discloses that translational efficiency in a rabbit        reticulocyte lysate system is greatest with mRNA transcribed        with an animal-type, followed by a mammalian-type, the        unnatural, and the plant-type cap structures, respectively, and        that G(5′)p₃Ampm⁷G-RNA, a result of transcribing in a reverse        orientation, was not obtained. Id.

In view of the disclosure of these publications, there remains a need toidentify modified cap structures that improve the efficiency of in vitrotranscription.

SUMMARY

Disclosed herein is a trinucleotide cap analog consisting ofm⁷G(5′)p₃-N₁pN₂, in which a m⁷G ribonucleotide is linked at its 5′-OH toa triphosphate bridge (p₃), wherein the triphosphate bridge is linked toa 5′-OH of ribonucleotide N₁, wherein N₁ is linked via its 3′-OH to aphosphate, wherein the phosphate is linked to a 5′-OH of a secondribonucleotide N₂, and wherein N₁ or N₂ or both consist of a modifiedbase or a modified ribose. The trinucleotide cap analogs describedherein provide improved transcriptional efficiency for in vitrosynthesis of capped mRNA, m⁷G(5′)p₃-RNA.

In one aspect, disclosed herein is a compound of formulam⁷G(5′)p₃(5′)N₁pN₂, wherein m⁷G is a ribonucleotide consisting ofN⁷-methylguanine and a ribose or a modified ribose wherein one or bothof the ribose 2′ or 3′ carbons has a fluoro or a C1-C6 alkoxysubstituent; (5′)p₃(5′) is a 5′ to 5′ triphosphate linkage, wherein thetriphosphate linkage may be substituted with one or morephosphorothioate groups; N₁ comprises a seco (UNA) ribose optionallysubstituted at the 2′ or 3′ carbons with one or more fluoro or C1-C6alkoxy substituents, and a base selected from the group consisting ofadenine, uridine, guanine, cytosine, N⁶-methyladenine, N¹-methyladenine,pseudouracil, N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil,2-thiouracil, 5-methyluracil, pseudoisocytosine, 5-methoxycytosine,2-thiocytosine, 5-hydroxycytosine, N⁴-methylcytosine,5-hydroxymethylcytosine, hypoxanthine, N¹-methylguanine,O⁶-methylguanine, N²-methylguanine (m²G), N²,N²-dimethylguanine(m^(2,2)G), N²,N′-dimethylguanine (m^(2,7)G), and isoguanine; whereinthe seco (UNA) ribose moiety is a seco (UNA) ribose or a modified seco(UNA) ribose, and wherein one or both of the seco (UNA) ribose 2′ or 3′carbons has a fluoro or a C1-C6 alkoxy substituent; and N₂ consists of(i) a base and (ii) a ribose moiety, wherein the base is selected fromthe group consisting of adenine, uridine, guanine, cytosine,N⁶-methyladenine, N¹-methyladenine, pseudouruacil,N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil, 2-thiouracil,5-methyluracil, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine,5-hydroxycytosine, N⁴-methylcytosine, 5-hydroxymethylcytosine,hypoxanthine, N¹-methylguanine, O⁶-methylguanine, N²-methylguanine(m²G), N²,N²-dimethylguanine (m^(2,2)G), N²,N′-dimethylguanine(m^(2,7)G), and isoguanine; wherein the m⁷G ribonucleotide is linked atits 5′-OH to the triphosphate bridge, wherein the triphosphate bridge islinked to a 5′-OH of the N₁ ribonucleotide, wherein N₁ nucleotide islinked via its 3′-OH to a phosphate, p, and wherein the phosphate islinked to a 5′-OH of the N₂ ribonucleotide; or a salt or solvated formthereof.

In some embodiments, the base of N₁ is adenine, uridine, guanine, orcytosine.

In some embodiments, the base of N₁ is adenine.

In some embodiments, the ribose moiety of N₁ consists of a modified seco(UNA) ribose and one or both of the ribose 2′ or 3′ carbons has a fluoroor a C1-C6 alkoxy substituent.

In some embodiments, the ribose moiety of N₁ consists of a modified seco(UNA) ribose and the 2′ carbon has a fluoro or a C1-C6 alkoxysubstituent.

In some embodiments, the ribose moiety of N₁ consists of a modified seco(UNA) ribose, wherein the ribose 2′ carbon has a C1-C6 alkoxysubstituent.

In some embodiments, the ribose moiety of N₁ consists of a modified seco(UNA) ribose, wherein the ribose 2′ carbon has a methoxy substituent.

In some embodiments, the base of N₂ is selected from the groupconsisting of guanine, N₁-methylguanine, O⁶-methylguanine, m²G,m^(2,2)G, m^(2,7)G, and isoguanine.

In some embodiments, the base of N₂ is guanine, N¹-methylguanine,O⁶-methylguanine, or isoguanine.

In some embodiments, the base of N₂ is guanine.

In some embodiments, the 2′ carbon of at least one ribose of m⁷G, N₁, orN₂ ribonucleotide is substituted by a C1-C6-alkoxy.

In some embodiments, at least one ribose of N₁ or N₂ ribonucleotide issubstituted by a 2′-O-methyl.

In some embodiments, the triphosphate bridge consists of 1, 2, or 3phosphorothioate groups.

In some embodiments, the compound is m⁷G(5′)p₃-seco-2′-OMeA-G, whereinseco-2′-OMeA is 2′-O-methyladenosine-seco(UNA)ribose and G is guanosine.

In another aspect, the compound increases the efficiency ofm⁷G(5′)p₃-RNA produced by in vitro transcription compared to3′-OMe-m⁷G(5′)p₃G.

In some embodiments, the in vitro transcription is mediated by T7 RNApolymerase or T6 RNA polymerase.

In another aspect, disclosed herein is a compound of formulam⁷G(5′)p₃(5′)N₁pN₂, wherein the compound increases the yield of5′-capped transcripts produced by in vitro transcription compared toACRA, (e.g., transcription is mediated by T7 RNA polymerase or T6 RNApolymerase).

In another aspect, disclosed herein is a compound of formulam⁷G(5′)ppp-N₁pN₂, wherein m⁷G is a ribonucleotide consisting ofN⁷-methylguanine and a ribose, wherein ppp is a 5′ to 5′ triphosphatelinkage; wherein N₁ comprises a seco (UNA) ribose optionally substitutedat the 2′ or 3′ carbons with one or more fluoro or C1-C6 alkoxysubstituents, and a base selected from the group consisting of adenine,uridine, guanine, cytosine, N⁶-methyladenine, N₁-methyladenine,pseudouracil, N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil,2-thiouracil, 5-methyluracil, pseudoisocytosine, 5-methoxycytosine,2-thiocytosine, 5-hydroxycytosine, N⁴-methylcytosine,5-hydroxymethylcytosine, hypoxanthine, N¹-methylguanine,O⁶-methylguanine, N²-methylguanine (m²G), N²,N²-dimethylguanine(m^(2,2)G), N²,N⁷-dimethylguanine (m^(2,7)G), and isoguanine; whereinthe seco (UNA) ribose moiety is a seco (UNA) ribose or a modified seco(UNA) ribose, and wherein one or both of the seco (UNA) ribose 2′ or 3′carbons has a fluoro or a C1-C6 alkoxy substituent; and N₂ consists of(i) a base and (ii) a ribose moiety, wherein the base is selected fromthe group consisting of adenine, uridine, guanine, cytosine,N⁶-methyladenine, N¹-methyladenine, pseudouruacil,N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil, 2-thiouracil,5-methyluracil, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine,5-hydroxycytosine, N⁴-methylcytosine, 5-hydroxymethylcytosine,hypoxanthine, N¹-methylguanine, O⁶-methylguanine, N²-methylguanine(m²G), N²,N²-dimethylguanine (m^(2,2)G), N²,N′-dimethylguanine(m^(2,7)G), and isoguanine; and wherein the m⁷G ribonucleotide is linkedat its 5′-OH to the triphosphate bridge, wherein the triphosphate bridgeis linked to a 5′-OH of the N₁ ribonucleotide, wherein N₁ nucleotide islinked via its 3′-OH to a phosphate, p, wherein the phosphate is linkedto a 5′-OH of the N₂ ribonucleotide; or a salt or solvated form thereof.

In some embodiments, the m⁷G ribonucleotide of the trinucleotide capanalog is modified so that the base is substituted with hypoxanthine,m⁷G, m⁶G, or isoguanine. In another aspect, one or both of the 2′-OH orthe 3′OH groups of the ribose group of the m⁷G ribonucleotide aresubstituted by fluoro or C1-C6 alkoxy group, or the ribose issubstituted by bicyclic (LNA) or seco (UNA) ribose.

In another aspect, disclosed herein is a method of synthesizing mRNA invitro from DNA by using the trinucleotide cap analog to initiatetranscription. In some embodiments, the in vitro transcription uses aDNA-dependent RNA polymerase (e.g., commercially available bacteriophageT7 RNA polymerase, T3 RNA polymerase, or SP6 RNA polymerase).

In another aspect, disclosed herein is an mRNA produced by in vitrotranscription using the trinucleotide cap analog. In some embodiments,disclosed herein is an mRNA produced the description herein thatinitiates translation of a protein. In some embodiments, disclosedherein is an mRNA produced by the methods herein that suppressestranslation of a protein. In some embodiments, disclosed herein is apharmaceutical composition comprising the mRNA described herein andpharmaceutical excipients. In some embodiments, the pharmaceuticalcomposition comprises the mRNA encapsulated in a liposomal nanoparticle.

In another aspect, disclosed herein is a method of treating a disease,comprising administering the pharmaceutical composition described hereinto a subject in need thereof.

In yet another aspect, disclosed herein is a kit comprising thetrinucleotide cap analog described herein. In some embodiments, the kitcomprises a T7 RNA polymerase, a T3 RNA polymerase, or a SP6 RNApolymerase.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows synthesis of m⁷GDP-IM (3) from GDP (1) by step i tointermediate m⁷GDP (2) and further imidazole addition at step ii.

FIG. 2 shows synthesis of 5′-O-DMT-2′O-Me-N⁶benzoyl-AMP-PhC (6) from2′OMe-adenosine (4) to first form a TMS-modified,benzoyl-m⁶-2′-OMe-adenosine which is benzoylated, then desilylated, andfurther protected as a DMTr ether (5) at step i. The introduction of thephosphate moiety (step ii) then gives 6.

FIG. 3 shows synthesis of 2′-O-Me, 3′-O-isobutyryl,N²-isobutyrylguanosine (9) from 2′OMe-guanosine (7) to produceintermediate N²-isobuyryl-2′-O-methylguanosine (8) in step i, in whichthe 5′-OH is protected as a DMTr ether, then the 3′-OH is isobutyrylatedand finally the DMTr group is removed in step ii to give 9.

FIG. 4 shows synthesis of protected 2′-OMeAp-2′-OMeG dinucleotide (10)in step i by reaction of 3′-p-2′-OMeA (6) with 2′OMe guanosine (9).

FIG. 5 shows removal of the protective groups of 2′OMeAp2′OMeGdinucleotide (10) in two steps: (i) to produce a 2′-OMeA-2′-OMeGdinucleotide compound 11 and phosphate introduction (ii) to produce2′OMeAp2′OMeG dinucleotide 5′-monophosphate (12).

FIG. 6 shows synthesis of m⁷G(5′)ppp2′OMeAp2′OMeG (13) by reaction (i)of the ammonium salt of pApG (12) with the sodium salt of m⁷GDP-IM (3).

FIG. 7 shows synthesis of m⁶-benzoyl-2′-OMe-AMP-PhCl (18) from2′OMe-adenosine (4) by first producing intermediate 15 (i), convertingto intermediate 16 (ii), forming TMS-modified, mono-benzoylatedm⁶2′OMe-adenosine which is desilylated to give (17) (iii), andprotection of the 5′-OH as a DMTr ether followed by phosphateintroduction (iv) gives 18.

FIG. 8 shows formation of dinucleotide m⁶2′OMeAp2′OMeG (21) by combiningbenzoyl-3′-p-m⁶2′-OMeA (18) with protected 2′OMe adenosine (9) toproduce intermediate m⁶2′OMeAp2′OMeG dinucleotide (19) in step i. Theprotective groups of m⁶2′OMeAp2′OMeG dinucleotide intermediate compoundare removed (ii) to produce m⁶2′OMeA-2′OMeG dinucleotide (20), which isphosphorylated (iii) to give 21.

FIG. 9 shows production of trinucleotide cap analog, m⁷G(5′)pppm⁶2′OMeAp2′OMeG (22) from the ammonium salt of pApG (21) and the sodiumsalt of m⁷GDP-IM (3).

FIG. 10 shows multistep synthesis of 2′-O,4′-C-methylene-linked bicyclicguanine nucleotide (32) from(3aS,6aS)-6-(benzyloxy)-2,2-dimethyltetrahydrofuro[2,3-d][1,3]dioxole-5,5-diyl)dimethanol(23). First (i) the diol is reacted with MsCl to yield intermediate(24), which is hydrolyzed and acetylated (ii) to produce the two isomersof intermediate (25). This intermediate is fused (iii) with butyratedguanine to produce a guanine nucleotide (26) as a precursor (iv) toproduction of bicycle guanine nucleotide 27. The 5′OMs of bicyclicguanine 27 benzoylated (v) to produce benzoate-intermediate 28, and isthen hydrolyzed (vi) to produce compound 29 having a free 5′OH.Intermediate 29 is further deprotected (vii) to obtain compound 30 withfree 3′ and 5′ OH groups. The 5′ OH group of compound 30 is blocked byDMTrCl (viii) to produce compound 31, which is acylated (viii) toproduce the locked guanyl nucleotide (32).

FIG. 11 shows synthesis of nucleotide m⁶2′OMeAp-locked-2′OMeG (35) by(i) combining locked guanyl nucleotide (32) with benzoylated3′-p-m⁶2′-OMeA (18) to produce intermediate dinucleotide (33). Thedinucleotide is deprotected (ii) to produce m⁶2′OMeA-locked-2′-OMeGdinucleotide (34), which is phosphorylated (iii) to give 35.

FIG. 12 shows synthesis of trinucleotide cap analog,m⁷G(5′)pppm⁶2′OMeAp-locked-2′-OMeG (36) by combining the ammonium saltof m⁶2′-OMeAp-locked-2′-OMeG dinucleotide 5′-monophosphate (35) with thesodium salt of m⁷GDP-IM (3)

FIG. 13 shows synthesis of 2′OMe-seco-3′-O-isobutyryl,N²-isobutyrylguanosine (43). The 5′ OH group of N²-isobutyrylguanosine(37) is blocked with DMTrCl to produce intermediate 38 (i), which isconverted (ii) to an “unlocked” form, 2′-O-benzoylated secoguanine (39).The 3′-OH group of the 2′-O-benzoylated secoguanine is protected byTBDMSCl (40). The 2′-O-benzoyl group of intermediate 40 is removed (iv)to yield the free 2′-OH group (41), which is methylated (v) to yieldintermediated 42. The silyl group is removed from the 3′-OH ofintermediate 42 and the 3-OH group is butyrylated (v) to producesecoguanine (43) after deblocking of the 5′-ODMTr ether.

FIG. 14 shows synthesis of p-2′-OMe-m⁶Ap-seco-2′-OMeG (46). Protected2′OMeAp2′OMeG dinucleotide (44) is produced by combining 3′-p-2′-OMeA(18) with protected 2′-OMe secoguanosine (43) to produce intermediate 44(i). The protective groups of intermediate 44 are removed (ii) toproduce a 2′-OMeA-2′-OMeG dinucleotide (45). The 5′-hydroxy group of theadenosine group is phosphorylated (iii) to produce2′-OMe-m⁶Ap-seco-2′-OMeG 5′-monophosphate (46).

FIG. 15 shows synthesis of trinucleotide cap analog,m⁷G(5′)pppm⁶2′-OMeAp-seco-2′-OMeG (47) from ammonium salt of2′-OMe-m⁶Ap-seco-2′-OMeG 5′-monophosphate (46) and the sodium salt ofm⁷GDP-IM (3).

FIG. 16 shows expression of m⁷G(5′)ppp-RNA transcribed from ARC CAP1(m⁷G(5′)p₃AmpG); ARCA (3′-OMe-m⁷G(5′)p₃G); or VACCINIA, without ARC CAP1or ARCA, by post-transcriptional capping by a vaccinia capping enzyme.

DETAILED DESCRIPTION

In order to increase the efficiency of in vitro transcription ofm⁷G(5′)p₃-RNA, the present description provides a trinucleotide capanalog, m⁷G(5′)p₃(5′)N₁pN₂.

In one aspect, disclosed herein is a compound of formulam⁷G(5′)p₃(5′)N₁pN₂, wherein m⁷G is a ribonucleotide consisting ofN⁷-methylguanine and a ribose or a modified ribose wherein one or bothof the ribose 2′ or 3′ carbons has a fluoro or a C1-C6 alkoxysubstituent; (5′)p₃(5′) is a 5′ to 5′ triphosphate linkage, wherein thetriphosphate linkage may be substituted with one or morephosphorothioate groups; N₁ comprises a seco (UNA) ribose optionallysubstituted at the 2′ or 3′ carbons with one or more fluoro or C1-C6alkoxy substituents, and a base selected from the group consisting ofadenine, uridine, guanine, cytosine, N⁶-methyladenine, N¹-methyladenine,pseudouracil, N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil,2-thiouracil, 5-methyluracil, pseudoisocytosine, 5-methoxycytosine,2-thiocytosine, 5-hydroxycytosine, N⁴-methylcytosine,5-hydroxymethylcytosine, hypoxanthine, N¹-methylguanine,O⁶-methylguanine, N²-methylguanine (m²G), N²,N²-dimethylguanine(m^(2,2)G), N²,N⁷-dimethylguanine (m^(2,7)G), and isoguanine; whereinthe seco (UNA) ribose moiety is a seco (UNA) ribose or a modified seco(UNA) ribose, and wherein one or both of the seco (UNA) ribose 2′ or 3′carbons has a fluoro or a C1-C6 alkoxy substituent; and N₂ consists of(i) a base and (ii) a ribose moiety, wherein the base is selected fromthe group consisting of adenine, uridine, guanine, cytosine,N⁶-methyladenine, N¹-methyladenine, pseudouruacil,N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil, 2-thiouracil,5-methyluracil, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine,5-hydroxycytosine, N⁴-methylcytosine, 5-hydroxymethylcytosine,hypoxanthine, N¹-methylguanine, O⁶-methylguanine, N²-methylguanine(m²G), N²,N²-dimethylguanine (m^(2,2)G), N²,N⁷-dimethylguanine(m^(2,7)G), and isoguanine; wherein the m⁷G ribonucleotide is linked atits 5′-OH to the triphosphate bridge, wherein the triphosphate bridge islinked to a 5′-OH of the N₁ ribonucleotide wherein N₁ nucleotide islinked via its 3′-OH to a phosphate, p, wherein the base of N₁ isadenine, and wherein the phosphate is linked to a 5′-OH of the N₂ribonucleotide; or a salt or solvated form thereof.

In another aspect disclosed herein is a compound of formulam⁷G(5′)p₃(5′)N₁pN₂, wherein m⁷G is a ribonucleotide consisting ofN⁷-methylguanine and a ribose; wherein (5′)p₃(5′) is a 5′ to 5′triphosphate linkage, and wherein N₁ and N₂ are ribonucleotides, whereinone or both of N¹ and N₂ consist of a base selected fromN⁶-methyladenine, N¹-methyladenine, pseudouruacil,N¹-methylpseudouracil, 5-iodouracil, 4-thiouracil, 2-thiouracil,5-methyluracil, pseudoisocytosine, 5-methoxycytosine, 2-thiocytosine,5-hydroxycytosine, N⁴-methylcytosine, 5-hydroxymethylcytosine,hypoxanthine, N¹-methylguanine, O⁶-methylguanine, 1-methyl-guanosine,N²-methyl-guanosine (m²G), N²,N²-dimethyl-guanosine (m^(2,2)G),2-methyl-2′-O-methyl-guanosine (m²Gm),N²,N²-dimethyl-2′-O-methyl-guanosine (m²²Gm),1-methyl-2′-O-methyl-guanosine, N²,N⁷-dimethyl-2′-O-methyl-guanosine(m^(2,7)Gm), or isoguanineadenine; and a ribose, a bicyclic (LNA)ribose, a seco (UNA) ribose, or a modified ribose wherein one or both ofthe ribose 2′ or 3′ carbons has a fluoro or a C1-C6 alkoxy substituent;and wherein the m⁷G ribonucleotide is linked at its 5′-OH to thetriphosphate bridge, wherein the triphosphate bridge is linked to a5′-OH of the N₁ ribonucleotide, wherein N₁ nucleotide is linked via its3′-OH to a phosphate, p, wherein the phosphate is linked to a 5′-OH ofthe N₂ ribonucleotide; or a salt or solvated form thereof.

One embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein N₁ is a ribonucleotideconsisting of adenine, uridine, guanine, or cytidine, preferablyadenine.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein N₂ consists ofN¹-methylguanine, O⁶-methylguanine, 1-methyl-guanosine, m²G, m^(2,2)G,m²Gm, m^(2,2)Gm, 1-methyl-2′-O-methyl-guanosine, m^(2,7)Gm, orisoguanineadenine.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein N₂ consists ofN¹-methylguanine, O⁶-methylguanine, or isoguanineadenine.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein N₁ consists of aLNA, a UNA, or a ribose wherein one or both of the ribose 2′ or 3′carbons has a fluoro or a C1-C6 alkoxy substituent.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein N₂ is aribonucleotide consisting of adenine, uridine, guanine, or cytidine,preferably guanine.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein N₂ is aribonucleotide consisting of a LNA, a UNA, or a ribose wherein one orboth of the ribose 2′ or 3′ carbons has a fluoro or a C1-C6 alkoxysubstituent.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ consists of m⁷G(5′)p₃AmpGm,wherein Am is 2′OMe-adenine and Gm is 2′OMe-guanine.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ consists of m⁷G(5′)p₃m⁶AmpGm,wherein ⁶mAm is 2′OMe-N⁶methyladenine and Gm is 2′OMe-guanine.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ consists ofm⁷G(5′)p₃m⁶AmpG_(LNA), wherein ⁶mAm is 2′OMe-N⁶methyladenine and G_(LNA)is guanine bicyclic (LNA)-ribose. Another embodiment is wherein at leastone ribose of the m⁷G, N₁, or N₂ ribonucleotide is a LNA.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ consists ofm⁷G(5′)p₃m⁶AmpG_(UNA), wherein ⁶mAm is 2′OMe-N⁶methyladenine and G_(U)NAis guanine seco(UNA)ribose. Another embodiment is wherein at least oneribose of m⁷G, N₁, or N₂ ribonucleotide is a UNA.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is, wherein at least one riboseof m⁷G, N₁, or N₂ ribonucleotide is substituted by a 2′-C1-C6-alkoxy,preferably 2′-OMe.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein the triphosphatebridge consisting of 1, 2, or 3 phosphorothioate groups.

Another embodiment of m⁷G(5′)p₃(5′)N₁pN₂ is wherein the compoundincreases the yield of 5′-capped transcripts produced by in vitrotranscription compared to ACRA, for example, transcription is mediatedby T7 RNA polymerase or T6 RNA polymerase.

Another aspect of the description is a compound of formulam⁷G(5′)ppp-N₁pN₂, wherein m⁷G is a ribonucleotide consisting ofN⁷-methylguanine and a ribose, wherein ppp is a 5′ to 5′ triphosphatelinkage; wherein N₁ and N₂ are ribonucleotides, wherein one or both ofN₁ and N₂ ribonucleotides consist of a base selected from adenine,uracil, cytosine, or guanine; and a bicyclic (LNA) ribose, a seco (UNA)ribose, or a modified ribose wherein one or both of the ribose 2′ or 3′carbons has a fluoro or a C1-C6 alkoxy substituent; and wherein the m⁷Gribonucleotide is linked at its 5′-OH to the triphosphate bridge,wherein the triphosphate bridge is linked to a 5′-OH of the N₁ribonucleotide wherein N₁ nucleotide is linked via its 3′-OH to aphosphate, p, wherein the phosphate is linked to a 5′-OH of the N₂ribonucleotide; or a salt or solvated form thereof.

In one aspect of the description, the m⁷G ribonucleotide of thetrinucleotide cap analog is modified so that the base is substitutedwith hypoxanthine, m¹G, m⁶G, or isoguanine. In another aspect, one orboth of the 2′-OH or the 3′OH groups of the ribose group of the m⁷Gribonucleotide are substituted by fluoro or C1-C6 alkoxy group, or theribose is substituted by bicyclic (LNA) or seco (UNA) ribose. In eithercase, the N₁ and N₂ ribonucleotides each consists of a baseindependently selected from adenine, uracil, cytosine, guanine, or ananalog thereof, and a sugar selected from ribose, modified ribose,bicyclic ribose, or seco ribose.

Another aspect of the description is a method of synthesizing mRNA invitro from DNA by using the trinucleotide cap analog according todescription herein to initiate transcription. In preferred embodiments,the in vitro transcription uses a DNA-dependent RNA polymerase (e.g.,commercially available bacteriophage T7 RNA polymerase, T3 RNApolymerase, or SP6 RNA polymerase).

Another aspect of the description is mRNA produced by in vitrotranscription using the trinucleotide cap analog described herein. Apreferred embodiment is an mRNA produced the description herein thatinitiates translation of a protein. Another preferred embodiment is anmRNA produced by the methods herein that suppresses translation of aprotein. Another embodiment is a pharmaceutical composition comprisingthe mRNA described herein and pharmaceutical excipients. In a preferredembodiment, the pharmaceutical composition comprises the mRNAencapsulated in a liposomal nanoparticle.

Another aspect of the description is a method of treating a disease,comprising administering the pharmaceutical composition described hereinto a subject in need thereof.

Another aspect of the description is a kit comprising the trinucleotidecap analog described herein. In a preferred embodiment, the kitcomprises a T7 RNA polymerase, a T3 RNA polymerase, or a SP6 RNApolymerase.

Definitions that follow will apply to the description herein. Wheneverappropriate, terms used in the singular will also include the plural andvice versa. In the event that any definition set forth below conflictswith the usage of that word in any other document, including anydocument incorporated herein by reference, the definition set forthbelow shall always control for purposes of interpreting thisspecification and its associated claims unless a contrary meaning isclearly intended (for example in interpreting the document where theterm is originally used). The use of “or” herein means “and/or” unlessstated otherwise or where the use of “and/or” is clearly inappropriate.The use of “a” herein means “one or more” unless stated otherwise orwhere the use of “one or more” is clearly inappropriate. The use of“comprise,” “comprises,” “comprising,” “include,” “includes,” and“including” are interchangeable and not intended to be limiting.

As used herein, “Me” means “CH₃”, and “OCH₃” or “OMe” denotes an oxygenatom bound to a methyl group, “CHO” denotes a carbon atom, C, bonded toa hydrogen atom, H, and double-bonded to an oxygen atom, O, (O═CH—) and“Et” denotes “C₂H₅”.

“Cap” herein means a non-extendible trinucleotide that facilitatestranslation or localization, and/or prevents degradation of an RNAtranscript when incorporated at the 5′ end of an RNA transcript. Itconsists in nature of the modified base 7-methylguanosine joined in theopposite orientation, 5′ to 5′ rather than 5′ to 3′, to the rest of theRNA molecule via three phosphate groups i.e., PI-guanosine-5′-ylP3-7-methylguanosine-5′-yl triphosphate (m⁷G5′ppp5′G).

“Hydrate” is a solvate wherein the solvent molecule is H₂O.

A “cap analog” means a structural derivative of an RNA cap that maydiffer by as little as a single element. Cap analog is used for thesynthesis of 5′ capped RNA molecules in in vitro transcriptionreactions. Substitution of cap analog for a portion of the GTP in atranscription reaction results in the incorporation of the cap structureinto a corresponding fraction of the transcripts. Capped mRNAs aregenerally translated more efficiently in reticulocyte lysate and wheatgerm in vitro translation systems. In vitro transcripts must be cappedfor microinjection experiments because uncapped mRNAs are rapidlydegraded. Cap analogs can also be used as a highly specific inhibitor ofthe initiation step of protein synthesis.

“Enzymatically incorporatable” means a nucleotide is capable of beingenzymatically incorporated onto the terminus, e.g. 3′ terminus, of apolynucleotide chain, or internally through nick-translation of apolynucleotide chain, through action of a template-dependent ortemplate-independent polymerase enzyme. A nucleotide-5′-triphosphate isan example of an enzymatically incorporatable nucleotide.

“Enzymatically extendable” or “3′ extendable” means a nucleotide orpolynucleotide that is capable of being appended to a nucleotide orpolynucleotide by enzyme action. A polynucleotide containing a 3′hydroxyl group is an example of an enzymatically extendablepolynucleotide.

A “locked nucleic acid” (LNA) means a ribonucleotide in which there is abridge between the 2′O and 4′C methylene bicyclonucleotide monomers.

A “nucleobase” means a nitrogen containing heterocyclic moietynucleobase. Non-limiting examples of suitable nucleobases include:adenine, cytosine, guanine, thymine, uracil, or analogs thereof, e.g.,5-propynyl-uracil, 2-thio-5-propynyl-uracil, 5-methylcytosine,pseudoisocytosine, 2-thiouracil, 2-thiothymine, 2-aminopurine,N9-(2-amino-6-chloropurine), N9-(2,6-diaminopurine), hypoxanthine,N9-(7-deaza-guanine), N9-(7-deaza-8-aza-guanine) andN8-(8-aza-7-deazaadenine).

A “ribonucleotide” or “nucleotide” herein means a compound consisting ofa nucleobase linked to the C-1′ carbon of a ribose sugar or analogthereof. The ribose or analog may be substituted or unsubstituted.Substituted ribose sugars include, but are not limited to, those ribosesin which one or more of the carbon atoms, preferably the 3′-carbon atom,is substituted with one or more of the same or different substituentssuch as —R, —OR, —NRR or halogen (e.g., fluoro, chloro, bromo, or iodo),where each R group is independently —H, C₁-C₆ alkyl or C₆-C₁₄ aryl orarylalkyl. Typically, when the nucleobase is A or G, the ribose sugar isattached to the N⁹-position of the nucleobase. When the nucleobase is C,T or U, the pentose sugar is attached to the N¹-position of thenucleobase. Examples of ribose analogs include arabinose, 2′-O-methylribose, UNA, and LNA analogs.

A “ribonucleotide” means a phosphate ester of a ribonucleotide as amonomer unit or within a polynucleotide.

A “nucleotide triphosphate” means a nucleotide with a triphosphate estergroup at the 5′ position.

“Alkyl”, “C1, C2, C3, C4, C5 or C6 alkyl” or “C1-C6 alkyl” is intendedto include C1, C2, C3, C4, C5 or C6 straight chain (linear) saturatedaliphatic hydrocarbon groups and C3, C4, C5 or e branched saturatedaliphatic hydrocarbon groups. For example, C1-C6 alkyl is intended toinclude C1, C2, C3, C4, C5 and C6 alkyl groups. Examples of alkylinclude, moieties having from one to six carbon atoms, such as, but notlimited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl,t-butyl, n-pentyl, s-pentyl or n-hexyl.

In certain embodiments, a straight chain or branched alkyl has six orfewer carbon atoms (e.g., C1-C6 for straight chain, C3-C6 for branchedchain), and in another embodiment, a straight chain or branched alkylhas four or fewer carbon atoms. Ribonucleotides and/or ribonucleotidescomprise ribose or a ribose analog.

“Ribose analog” includes, e.g., substituted or unsubstituted furanoseshaving more or fewer than 5 ring atoms, e.g., erythroses and hexoses andsubstituted or unsubstituted 3-6 carbon acyclic sugars (e.g., UNA).Typical substituted furanoses and acyclic sugars are those in which oneor more of the carbon atoms are substituted with one or more of the sameor different —R, —OR, —NRR or halogen groups, where each R isindependently —H, (C₁-C₆) alkyl or (C₁-C₁₄) aryl. Examples ofsubstituted furanoses having 5 ring atoms include but are not limited to2′-deoxyribose, 2′-(C₁-C₆)alkylribose, 2′-(C₁-C₆)alkoxyribose,2′-(C₅-C₁₄)aryloxyribose, 2′,3′-dideoxyribose, 2′,3′-didehydroribose,2′-deoxy-3′-haloribose, 2′-deoxy-3′-fluororibose,2′-deoxy-3′-chlororibose, 2′-deoxy-3′-aminoribose,2′-deoxy-3′-(C₁-C₆)alkylribose, 2′-deoxy-3′-(C₁-C₆)alkoxyribose,2′-deoxy-3′-(C₅-C₁₄)aryloxyribose,3′-(C₁-C₆)alkylribose-5′-triphosphate,2′-deoxy-3′-(C₁-C₆)alkylribose-5′-triphosphate,2′-deoxy-3′-(C₁-C₆)alkoxyribose-5′-triphosphate,2′-deoxy-3′-(C₅-C₁₄)atyloxyribose-5′-triphosphate,2′-deoxy-3′-haloribose-5′-triphosphate,2′-deoxy-3′-aminoribose-5′-triphosphate,2′,3′-dideoxyribose-5′-triphosphate or2′,3′-didehydroribose-5′-triphosphate. Further sugar analogs alsoinclude so called locked nucleic acids (LNAs) having the structure

and those described in WO 99/14226 and Koskin, 2001, J Org Chem,66:8504-12 (incorporated herein by reference) and unlocked ribonucleicacid (UNA) having the structure

and those described in U.S. Pat. Nos. 9,297,009 and 9,051,570(incorporated herein by reference).

“Polynucleotide”, “oligonucleotide” and “nucleic acid” mean singlestranded or double stranded polymers of nucleotide monomers, includingribonucleotides (RNA) and 2′-deoxyribonucleotides (DNA) linked byinternucleotide phosphodiester bond linkages. A polynucleotide may becomposed entirely of deoxyribonucleotides, entirely of ribonucleotidesor chimeric mixtures thereof.

“Substituted” means substitution with specified groups other thanhydrogen, or with one or more groups, moieties or radicals which can bethe same or different, with each, for example, being independentlyselected.

The trinucleotide compounds of described herein form salts that are alsowithin the scope of this disclosure. Reference to a trinucleotidecompound herein is understood to include reference to salts thereof,unless otherwise indicated.

“Salt(s)” mean acidic salts formed with inorganic and/or organic acids,as well as basic salts formed with inorganic and/or organic bases. Inaddition, when a trinucleotide compound contains both a basic moiety,such as, but not limited to a pyridine or imidazole, and an acidicmoiety, such as, but not limited to a carboxylic acid, zwitterions(“inner salts”) may be formed and are included within the term “salt(s)”as used herein. The salts can be pharmaceutically acceptable (i.e.,non-toxic, physiologically acceptable) salts, although other salts arealso useful. Salts of the trinucleotide compounds may be formed, forexample, by reacting the trinucleotide compounds with an amount of acidor base, such as an equivalent amount, in a medium such as one in whichthe salt precipitates or in an aqueous medium followed bylyophilization.

Exemplary acid addition salts include acetates, adipates, alginates,ascorbates, aspartates, benzoates, benzenesulfonates, bisulfates,borates, butyrates, citrates, camphorates, camphorsulfonates,cyclopentanepropionates, digluconates, dodecylsulfates,ethanesulfonates, fumarates, glucoheptanoates, glycerophosphates,hemisulfates, heptanoates, hexanoates, hydrochlorides, hydrobromides,hydroiodides, 2-hydroxyethanesulfonates, lactates, maleates,methanesulfonates, benzenesulfonates, toluenesulfonates, nitrobenzenesulfonates, 2-napthalenesulfonates, nicotinates, nitrates, oxalates,pectinates, persulfates, 3-phenylpropionates, phosphates, picrates,pivalates, propionates, salicylates, succinates, sulfates, sulfonates(such as those mentioned herein), tartarates, thiocyanates,toluenesulfonates (also known as tosylates) undecanoates, and the like.Additionally, acids which are generally considered suitable for theformation of pharmaceutically useful salts from basic pharmaceuticalcompounds. These disclosures are incorporated herein by referenceherein.

Exemplary basic salts include ammonium salts, alkali metal salts such assodium, lithium, and potassium salts, alkaline earth metal salts such ascalcium and magnesium salts, salts with organic bases (for example,organic amines) such as benzathines, dicyclohexylamines, hydrabamines(formed with N,N-bis(dehydroabietyl)ethylenediamine),N-methyl-D-glucamines, N-methyl-D-glucamides, t-butyl amines, trialkylamines such as triethyl amine, and salts with amino acids such asarginine, lysine and the like. Basic nitrogen-containing groups may bequarternized with agents such as lower alkyl halides (e.g., methyl,ethyl, propyl, and butyl chlorides, bromides and iodides), dialkylsulfates (e.g., dimethyl, diethyl, dibutyl, and diamyl sulfates), longchain halides (e.g., decyl, lauryl, myristyl, and stearyl chlorides,bromides and iodides), arylalkyl halides (e.g., benzyl and phenethylbromides), allylic and propargylic halides such as 1-bromo-2-propene and1-bromo-2-propyne, and others.

All such acid and base salts are intended to be pharmaceuticallyacceptable salts within the scope of the disclosure and all acid andbase salts are considered equivalent to the free forms of thecorresponding compounds for purposes of the disclosure.

“Solvate” means a physical association of a trinucleotide compound ofthis disclosure with one or more solvent molecules. This physicalassociation involves varying degrees of ionic and covalent bonding,including hydrogen bonding. In certain instances, the solvate will becapable of isolation, for example when one or more solvent molecules areincorporated in the crystal lattice of the crystalline solid. Solvateencompasses both solution-phase and isolatable solvates. Non-limitingexamples of suitable solvates include water, ethanolates, methanolates,and the like. Trinucleotide compounds of the disclosure can exist inunsolvated and solvated forms, including hydrated forms. In general, thesolvated forms, with pharmaceutically acceptable solvents such as water,ethanol and the like, are equivalent to the unsolvated forms for thepurposes of this disclosure.

Trinucleotide compounds of the disclosure, and solvates thereof, mayexist in their tautomeric form. All such tautomeric forms arecontemplated herein as part of the present disclosure.

All stereoisomers (for example, geometric isomers, optical isomers andthe like) of the present trinucleotide compounds (including those of thesalts, solvates and prodrugs of the trinucleotide compounds as well asthe salts and solvates of the prodrugs), such as those which may existdue to asymmetric carbons on various substituents, includingenantiomeric forms (which may exist even in the absence of asymmetriccarbons), rotameric forms, atropisomers, and diastereomeric forms, arecontemplated within the scope of this disclosure. Individualstereoisomers of the trinucleotide compounds of this disclosure may, forexample, be substantially free of other isomers, or may be admixed, forexample, as racemates or with all other, or other selected,stereoisomers. The chiral centers of the trinucleotide compounds hereincan have the S or R configuration as defined by the IUPAC 1974Recommendations. The use of the terms “salt”, “solvate”, and the like,is intended to equally apply to the salt, solvate and prodrug ofenantiomers, stereoisomers, rotamers, tautomers, or racemates of thedisclosed trinucleotide compounds.

The trinucleotide compounds of the disclosure may also contain unnaturalproportions of atomic isotopes at one or more of the atoms thatconstitute such trinucleotide compounds. Unnatural proportions of anisotope may be defined as ranging from the amount found in nature to anamount consisting of 100% of the atom in question. For example, thetrinucleotide compounds may incorporate radioactive isotopes, such as,for example, tritium (³H), iodine-125 (¹²⁵I) or carbon-14 (¹⁴C), ornon-radioactive isotopes, such as deuterium (²H), carbon-13 (¹³C), orisotopes of nitrogen, oxygen and sulfur. Such isotopic variations canprovide additional utilities to those described elsewhere within thisapplication. For instance, isotopic variants of the trinucleotidecompounds of the invention may find additional utility, including butnot limited to, as diagnostic and/or imaging reagents, or ascytotoxic/radiotoxic therapeutic agents. Additionally, isotopic variantsof the trinucleotide compounds of the invention can have alteredpharmacokinetic and pharmacodynamic characteristics which can contributeto enhanced safety, tolerability or efficacy during treatment. Allisotopic variations of the trinucleotide compounds of the descriptionherein, whether radioactive or not, are intended to be encompassedwithin the scope of the description herein.

“Inhibitors” and “antagonists”, or “activators” and “agonists” meaninhibitory or activating molecules, respectively, for example, for theactivation of, e.g., a ligand, receptor, cofactor, gene, cell, tissue,or organ. Inhibitors are molecules that decrease, block, prevent, delayactivation, inactivate, desensitize, or down-regulate, e.g., a gene,protein, ligand, receptor, or cell. Activators are molecules thatincrease, activate, facilitate, enhance activation, sensitize, orup-regulate, e.g., a gene, protein, ligand, receptor, or cell. Aninhibitor may also be defined as a molecule that reduces, blocks, orinactivates a constitutive activity. An “agonist” is a molecule thatinteracts with a target to cause or promote an increase in theactivation of the target. An “antagonist” is a molecule that opposes theaction(s) of an agonist. An antagonist prevents, reduces, inhibits, orneutralizes the activity of an agonist, and an antagonist can alsoprevent, inhibit, or reduce constitutive activity of a target, e.g., atarget receptor, even where there is no identified agonist.

The “activity” of a molecule may describe or refer to the binding of themolecule to a ligand or to a receptor; to catalytic activity; to theability to stimulate gene expression or cell signaling, differentiation,or maturation; to antigenic activity; to the modulation of activities ofother molecules; and the like.

“Proliferative activity” means an activity that promotes, that isnecessary for, or that is specifically associated with, for example,normal cell division, as well as cancer, tumors, dysplasia, celltransformation, metastasis, and angiogenesis.

mRNA Synthesis

The trinucleotide cap analogs disclosed herein are used for improvingthe synthesis of 5′ capped RNA molecules in in vitro transcriptionreactions. Substitution of cap analog for a portion of the GTP in atranscription reaction results in the incorporation of the cap structureinto a corresponding fraction of the transcripts.

Transcription of RNA usually starts with a nucleotide triphosphate(usually a purine, A or G). When transcription occurs in vitro, ittypically includes a phage RNA polymerase such as T7, T3 or SP6, a DNAtemplate containing a phage polymerase promoter, nucleotides (ATP, GTP,CTP and UTP) and a buffer containing magnesium salt. The synthesis ofcapped RNA includes the incorporation of a cap (e.g., m⁷GpppG) or a capanalog (such as those described herein) in the transcription reaction.Excess cap to GTP (e.g., 4:1) increases the opportunity that eachtranscript will have a 5′ cap. The mMESSAGE mMACHINE® SP6 TranscriptionKit and SP7 Ultra Kit (ThermoFisher Scientific) recommends this ratioand will typically yield 80% capped RNA to 20% uncapped RNA, althoughtotal yields of total RNA are lower as GTP concentration becomes ratelimiting as GTP is necessary for the elongation of the transcript.

Capped mRNAs are generally translated more efficiently in reticulocytelysine and wheat germ in vitro translation systems. It is important thatin vitro transcripts be capped for microinjection experiments becauseuncapped mRNAs are rapidly degraded. Cap analogs are also used as ahighly specific inhibitor of the initiation step of protein synthesis.

The 5′ cap structure enhances the translation of mRNA by helping to bindthe eukaryotic ribosome and assuring recognition of the proper AUGinitiator codon. This function may vary with the translation system andwith the specific mRNA being synthesized. The consensus sequence5′-GCCACCAUGG-3′, also known as the “Kozak” sequence, is considered tobe the strongest ribosomal binding signal in eukaryotic mRNA. Forefficient translation initiation, the key elements are the 5′ G residueat the +1 position and the A residue at the 3′ position of the mRNA.

The mRNA can be transfected into a cell to be translatedintracellularly. Methods of transfection are known to those of skill inthe art and include microinjection, electroporation, chemical treatmentsand the like. Cells for use in in vivo translation include any patientcell for which it is desired to express a protein of interest. Cellsinclude hematopoietic cells (e.g., T cells, dendritic cells,macrophages, etc.), bone marrow cells, tissue culture cells, germ cells,and the like.

Compositions comprising modified capped RNA as described herein can beused for in vitro transcription, in vitro translation, and in vivotranslation, for example. Current biotechnology efforts for in vitro, insitu, and in vivo protein production will also benefit from thesemethods and compositions. Further, compositions provided herein areuseful for therapeutic purposes. For example, the present technology maybe useful for generating vaccines against infectious diseases orcancers. Alkyne-derivatized capped RNA can be used to producenon-infectious particles of Venezuelan Equine Encephalitis viruscontaining an RNA encoding immunogen. These non-replicating viralparticles can be injected into humans where they can enter host cells.Once in the host cell, the viral particles dissociate and the mRNAencoding the immunogen is translated into protein. These proteins caninduce an immune response. These types of vaccines are expected to beuseful for human immunodeficiency virus (HIV), feline immunodeficiencyvirus, human papilloma virus type 16, tumors, lassa virus, Ebola virus,Marburg virus, anthrax toxin from Bacillus anthraces, and botulinumtoxin. These vaccine strategies can require large quantities of cappedRNA. The present methods facilitate such synthesis and subsequentpurification of capped RNA so as to make these vaccines commerciallyfeasible. As well, strategies to increase the percentage of full lengthcapped RNA in a transcription reaction leading to a more homogenousproduct will be preferred in the vaccine industry as highly purecomponents are usually required for human use. In addition, researchersprefer to use products that are as pure as possible to minimize thenumber of variables in an experiment. As well, the purer the product,the more potent it is.

Such oligomers or oligonucleotides may be prepared by solid statesynthesis or by other means known to those skilled in the art. Forexample, 2′-O-alkyl guanosine phosphoramidites and derivatives thereofmay be incorporated into oligonucleotides using standard phosphoramiditechemistry. Incorporation of 2′-O-alkyl guanosine nucleotides may conferdesirable characteristics to an oligonucleotide such as enhancedresistance to nuclease.

“Oligonucleotide” or “oligomer” as used herein means a polynucleotideformed from naturally occurring bases and furanosyl groups joined bynative phosphodiester bonds. Oligonucleotides of the description hereinwill, of course, comprise at least one 2′-O-alkyl guanosine orderivative thereof. Thus, this term effectively refers to naturallyoccurring species or synthetic species formed from naturally occurringsubunits or their close homologs. The term “oligonucleotide” or“oligomer” may also refer to moieties which have portions similar tonaturally occurring oligonucleotides, but which have non-naturallyoccurring portions. Thus, oligonucleotides may have altered sugars,altered base moieties, or altered inter-sugar linkages. Exemplary amongthese are the phosphorothioate and other sulfur-containing species whichare known for use in the art. In accordance with some preferredembodiments, at least some of the phosphodiester bonds of theoligonucleotide have been substituted with a structure which functionsto enhance the stability of the oligonucleotide or the ability of theoligonucleotide to penetrate into the region of cells where themessenger RNA is located. It is preferred that such substitutionscomprise phosphorothioate bonds, phosphotriesters, methyl phosphonatebonds, short chain alkyl or cycloalkyl structures or short chainheteroatomic or heterocyclic structures. Other preferred substitutionsare CH₂—NH—O—CH₂, CH₂—N(CH₃)—O—CH₂, CH₂—O—N(CH₃)—CH₂,CH₂—N(CH₃)—N(CH₃)—CH₂ and O—N(CH₃)—CH₂—CH₂ structures wherephosphodiester intersugar linkage is replaced by the substitutions. Alsopreferred are morpholino structures. In accordance with other preferredembodiments, the phosphodiester bonds are substituted with otherstructures which are, at once, substantially non-ionic and non-chiral,or with structures which are chiral and enantiomerically specific.Persons of ordinary skill in the art will be able to select otherlinkages for use in practice of the invention.

Oligonucleotides may also include species which include at least somemodified base forms. Thus, purines and pyrimidines other than thosenormally found in nature may be so employed. Suitable bases includemodifications on the furanosyl portion of the nucleotide subunits, inaddition to 2′-O-alkyl modifications of the description herein, may alsobe effected as long as the essential tenets of this invention areadhered to. Examples of such modifications are 2′-halogen-substitutednucleotides. Some specific examples of modifications at the 2′ positionof sugar moieties which are useful in the description herein are OH, SH,SCH₃, F, OCN, O(CH₂)_(n)NH₂, Cl, Br, CN, CF₃, OCF₃, S—, OC1-OC12,O-alkenyl, O-alkynal, or N-alkyl; S- or N-alkenyl; SOCH₃, SO₂CH₃; ONO₂;NO₂; N₃; NH₂; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino;polyalkylamino; substituted silyl; an RNA cleaving group; a conjugate; areporter group; an intercalator; a group for improving thepharmacokinetic properties of an oligonucleotide; or a group forimproving the pharmacodynamic properties of an oligonucleotide and othersubstituents having similar properties. Sugar mimetics such ascyclobutyls may also be used in place of the pentofuranosyl group.Oligonucleotides may also comprise other modifications consistent withthe spirit of this invention. Such oligonucleotides are best describedas being functionally interchangeable with yet structurally distinctfrom natural oligonucleotides. All such oligonucleotides arecomprehended by this invention so long as they effectively function assubunits in the oligonucleotide.

Preferably oligonucleotides of the description herein are from about 6to about 50 nucleotides in length. In still more preferred embodimentsof the description herein oligonucleotides are from about 12 to about 20nucleotides in length.

Intercalators are molecules which insert themselves between neighboringbases of an oligonucleotide, e.g., acridine.

Reporter molecules are molecules which may aid in the identification ofa molecule, either visually or otherwise. For example, biotin andvarious fluorophores are effective reporter groups.

Conjugates, or bifunctional linkers effectively join two groups. Someconjugates are commercially available such as biotin or 3′maleimidobenzoyl-N-hydroxy-succinimide.

Pharmacodynamic property improvement means, in this context, improvedoligonucleotide uptake, enhanced oligonucleotide resistance todegradation, and/or strengthened sequence-specific hybridization withRNA. Such groups do not initiate chemical reactions. Groups that enhancethe pharmacodynamic properties of an oligonucleotide preferably includealkyl chains, polyamines, ethylene glycols, polyamides, alkyl chains,aminoalkyl chains and amphipathic moieties. Pharmacokinetic propertyimprovement means improved oligonucleotide uptake, distribution,metabolism or excretion.

Antisense therapy involves the use of oligonucleotides which arespecifically hybridizable to target RNA or DNA. Oligonucleotides of thedescription herein are preferably specifically hydridizable with atarget region. “Specifically hybridizable” means capable of forming astable duplex with a target DNA or RNA. Upon binding to, or forming astable duplex with, the target RNA or DNA, the antisense oligonucleotidecan selectively inhibit the genetic expression of these nucleic acids orcan induce some other events such as destruction of a targeted RNA orDNA or activation of gene expression. Destruction of targeted RNA can beeffected by RNase H activation or by linking strand cleavers to theoligonucleotide.

In some embodiments of the description herein the oligonucleotideportions of trinucleotide compounds of the description herein are atleast 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% complementary to atarget sequence. In preferred embodiments of the description herein theoligonucleotide portions of trinucleotide compounds of the descriptionherein are at least 60%, 70%, or 80% complementary to a target sequence.100% complementarity of the oligonucleotide portions of trinucleotidecompounds of the description herein to a target sequence is mostpreferred. In preferred embodiments of the description herein, theoligonucleotide portions may be specifically hybridizable with DNA orRNA from Candida, papilloma virus, Epstein Barr virus, rhinovirus,hepatitis, human immunodeficiency virus, herpes simplex virus, influenzavirus and cytomegalovirus.

2-O-alkyl guanosine containing oligonucleotides of the descriptionherein may be used to modulate the production of protein by contacting aselected sequence of RNA or DNA coding for a selected protein with an2′-O-alkyl guanosine containing oligonucleotide of the descriptionherein having a sequence of nucleotide bases specifically hybridizablewith said selected sequence of RNA or DNA coding for said protein.

The oligonucleotides of the description herein can be used indiagnostics, therapeutics and as research reagents. For therapeutic use,an animal having a disease characterized by the undesired production ofa protein is contacted with an oligonucleotide of the description hereinhaving a sequence of nucleotide bases specifically hybridizable with aselected sequence of RNA or DNA coding for said protein.

Pharmaceutical Use

Another use of compositions described herein involves isolatingdendritic cells (DCs) from a patient and then transfecting the dendriticcells with derivatized capped RNA as described herein encodingimmunogen. The dendritic cells translate the derivatized capped RNA intoat least one protein that induces an immune response against thisprotein.

Morse, 2002, Int J Gastrointest Cancer, 32:1-6, discloses thatimmunotherapy with dendritic cells loaded with CEA capped RNA is safeand feasible for pancreatic cancer patients. Heiser, 2002, J ClinInvest, 109:409-17, discloses that introducing at least one singlecapped RNA species into immature dendritic cells induced a specificT-cell response. The cap analogs provided herein can be used forproviding mRNAs for antigen delivery to DCs for the purpose ofimmunotherapy against cancer and infectious diseases.

Other uses include reprogramming differentiated cells to pluripotencyand/or to re-program pluripotent cells using capped RNA described hereinto specifically differentiate cell types by continuous transfection ofspecific derivatized-capped mRNAs over a time-period necessary forchanging the cell differentiation.

Trinucleotide compounds of the disclosure may be in the form ofcompositions suitable for administration to a subject. In general, suchcompositions are “pharmaceutical compositions” comprising at least onetrinucleotide compound and one or more pharmaceutically acceptable orphysiologically acceptable diluents, carriers or excipients. In certainembodiments, trinucleotide compounds of the disclosure are present in atherapeutically acceptable amount. The pharmaceutical compositions maybe used in the methods of the description herein; thus, for example, thepharmaceutical compositions can be administered ex vivo or in vivo to asubject in order to practice the therapeutic and prophylactic methodsand uses described herein.

The pharmaceutical compositions of the description herein can beformulated to be compatible with the intended method or route ofadministration; exemplary routes of administration are set forth herein.Furthermore, the pharmaceutical compositions may be used in combinationwith other therapeutically active agents or trinucleotide compounds asdescribed herein in order to treat or prevent the diseases, disordersand conditions as contemplated by the description herein.

The description herein contemplates the administration of trinucleotidecompounds of the disclosure, and compositions thereof, in anyappropriate manner. Suitable routes of administration include oral,parenteral (e.g., intramuscular, intravenous, subcutaneous (e.g.,injection or implant), intraperitoneal, intracisternal, intraarticular,intraperitoneal, intracerebral (intraparenchymal) andintracerebroventricular), nasal, vaginal, sublingual, intraocular,rectal, topical (e.g., transdermal), sublingual and inhalation.

Trinucleotide compounds of the disclosure may be administered to asubject in an amount that is dependent upon, for example, the goal ofadministration (e.g., the degree of resolution desired); the age,weight, sex, and health and physical condition of the subject to whichthe formulation is being administered; the route of administration; andthe nature of the disease, disorder, condition or symptom thereof. Thedosing regimen may also take into consideration the existence, nature,and extent of any adverse effects associated with the agent(s) beingadministered. Effective dosage amounts and dosage regimens can readilybe determined from, for example, safety and dose-escalation trials, invivo studies (e.g., animal models), and other methods known to theskilled artisan.

In general, dosing parameters dictate that the dosage amount be lessthan an amount that could be irreversibly toxic to the subject (themaximum tolerated dose (MTD)) and not less than an amount required toproduce a measurable effect on the subject. Such amounts are determinedby, for example, the pharmacokinetic and pharmacodynamic parametersassociated with ADME, taking into consideration the route ofadministration and other factors.

An effective dose (ED) is the dose or amount of an agent that produces atherapeutic response or desired effect in some fraction of the subjectstaking it. The “median effective dose” or ED50 of an agent is the doseor amount of an agent that produces a therapeutic response or desiredeffect in 50% of the population to which it is administered. Althoughthe ED50 is commonly used as a measure of reasonable expectance of anagent's effect, it is not necessarily the dose that a clinician mightdeem appropriate taking into consideration all relevant factors. Thus,in some situations the effective amount is more than the calculatedED50, in other situations the effective amount is less than thecalculated ED50, and in still other situations the effective amount isthe same as the calculated ED50.

The amount and frequency of administration of the trinucleotidecompounds of this disclosure and/or the pharmaceutically acceptablesalts thereof will be regulated according to the judgment of theattending clinician considering such factors as age, condition and sizeof the patient as well as severity of the symptoms being treated.

EXAMPLES

Aspects of the present teachings may be further understood in light ofthe following examples, which should not be construed as limiting thescope of the present teachings in any way.

While the present teachings are described in conjunction with variousembodiments, it is not intended that the present teachings be limited tosuch embodiments. On the contrary, the present teachings encompassvarious alternatives, modifications, and equivalents, as will beappreciated by those of skill in the art.

Example 1

2-amino-9-((2S,3R,4S,5S)-3,4-dihydroxy-5-(((hydroxy((hydroxy(1H-imidazol-1-yl)phosphoryl)oxy)phosphoryl)oxy)methyl)tetrahydrofuran-2-yl)-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium(m⁷GDP-IM, FIG. 1, compound 3). Synthesis of m⁷GDP-IM from GDP is doneby a two-step process according to Piecyk, 2012, Tetrahedron Letters,53:4843-47 (hereby incorporated by reference), First, GDP (compound 1)is reacted with methyl iodide in DMSO to produce m⁷GDP (compound 2, stepi). One equivalent of m⁷GDP is combined with 20 equivalents ofimidazole, 2 equivalents of 2,2′-dithiophyridine, and triethylamine inanhydrous dimethylformamide (DMF) and stirred for 6-8 hours at roomtemperature (step ii). The imidazole product is precipitated from asolution of anhydrous sodium perchlorate in dry acetone and, aftercooling to 4° C., the precipitate is filtered, washed in acetone, anddried overnight under vacuum to yield m⁷GDP-IM (compound 3).

Example 2

(2R,3S,4S,5R)-5-(6-benzamido-9H-purin-9-yl)-2-(hydroxy-DMT)-4-methoxytetrahydrofuran-3-yl(4-chlorophenyl) phosphate (5′-O-DMT-2′O-Me-N⁶benzoyl-AMP-PhCl, FIG. 2,compound 6) is prepared in two steps. First, commercially available2′OMe-adenosine (compound 4) is reacted with benzoyl chloride inpyridine to acylate N⁶ by the method of Zhu, 2003, SyntheticCommunications, 33:1233-43 (hereby incorporated by reference).2′OMe-adenosine is reacted with 1.1 equivalents of TMSCl per OH grouptogether with 1.2 equivalents of benzoyl chloride to produceTMS-modified, benzoyl-m⁶-2′-OMe-adenosine. The TMSA groups are removedunder aqueous acidic conditions in THF-TFA. Further, the 5′-hydroxy ofbenzoyl-m⁶-2′-OMe-adenosine is reacted with DMT to form an ether (stepii) (compound 5) according to the method of WO 99/14266 (herebyincorporated by reference) by preparing a anhydrous pyridine solution ofthe nucleotide, adding an excess of 4,4′-dimethoxytrityl chloride,stirring at room temperature for 2 hours, quenching the reaction withice cold water, and extracting the product with DCM. The combinedorganic phases are washed with NaHCO₃-saturated water, brine, and driedNa₂SO₄. Phosphorylated adenosine is produced from DMT protected compound5 by the method of Lewdorowicz, 2007, Nucleotides, Nucleotides, andNucleic Acids, 26:1339-48 (hereby incorporated by reference) by reactionwith 4-chlorophenyl dichlorophosphate as a 3′-O-phosphorylating agent(step ii) to produce 5′O-DMT-2′-O-Me-N⁶benzoyl-AMP-PhCl (compound 6).

Example 3

(2R,3S,4S,5R)-2-(hydroxymethyl)-4-methoxy-5-(6-oxo-2-propionamido-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-3-ylisobutyrate (2′-O-Me,3′-O-isobutyryl,N²-isobutyrylguanosine; FIG. 3,compound 9). Compound 9 is synthesized by the method of U.S. Pat. No.7,101,993 (hereby incorporated by reference) from commercially available2′OMe-guanosine (FIG. 7, step i). 2′-O-methylguanosine (compound 7) inpyridine is cooled in an ice bath and 6 equivalents of trimethylsilylchloride (TMSCl) is added and mixed for 30 minutes, and isobutyrylchloride is added and stirred for 4 hours. Water is added and themixture is stirred for 30 minutes and concentrated NH₄OH is added andthe solution is evaporated in vacuo to produce theN²-isobuyryl-2′-O-methylguanosine compound 8. The 5′-hydroxy group isprotected with a DMT group, the 3′-hydroxy group is subject toisobutyrylation, and the DMT group is removed by treatment with 5%trichloroacteic acid to produce protected 2′OMe guanine compound 9 (stepii).

Example 4

((2R,3S,4S,5R)-3-(((((2R,3S,4S,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxy-4-methoxytetrahydrofuran-2-yl)methoxy)oxidophosphoryl)oxy)-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl)methylhydrogen phosphate (p-2-′OMeAp-2′-OMeG, FIG. 5, compound 12). Protected2′OMeAp2′OMeG dinucleotide, compound 10 (FIG. 4), was produced bycombining 3′-p-2′-OMeA compound 6 (Example 2) with protected 2′-OMeguanosine compound 9 (Example 3) by the method of Lewdorowicz 2007.First, 3′-p-2′-OMeA compound 6 was mixed with an equivalent of 2′OMeguanosine compound 9 in anhydrous acetonitrile and the mixture was driedby evaporation. A solution of 2,4,6,-triisopropylbenzenesulfonylchloride and N-methylimidazole in acetonitrile was added and the mixturewas reacted for 4 hours to produce the protected 2′-OMeAp-2′-OMeGdinucleotide compound 10 (FIG. 4, step i).

The protective groups of 2′OMeAp2′OMeG dinucleotide compound 10 wereremoved (FIG. 5, step i) using known reactions, e.g., by a methodselected from Lewdorowicz 2007; Huss, 1988, J Org Chem, 53:499-506;Zhou, 1986, Tetrahedron, 42:4149-56; Reese, 1986, Tetrahedron Letters,27:2291-94; Abramova, 2008, Biorg Med Chem, 16:9127-32; Abramova, 2013,Beilstein J Org Chem, 9:2898-909; Hashmi, 1994, Nucleotides &Nucleotides, 13:1059-67; Hsu, 1985, Nucleotides & Nucleotides, 4:377-89;Puech, 1988, J Med Chem, 31:1897-907 (hereby incorporated by reference)(FIG. 5, step i) were removed to produce a 2′-OMeA-2′-OMeG dinucleotidecompound 11. The 5′-hydroxy group of the adenosine group wasphosphorylated according to the method of Lewdorowicz 2007 (FIG. 5, stepii). Phosphorus trichloride oxide in trimethyl phosphate was cooled to4° C. and the 5′-O-guanine-adenine dinucleotide-3′-O compound 10 wasadded and stirred at 4° C. for 3 hours. Tetraethylammoniuum bromide(TEAB) was added to neutralize the mixture to produce the 2′OMeAp2′OMeGdinucleotide 5′-monophosphate (FIG. 5, compound 12).

Example 5

Trinucleotide Cap Analog, m⁷G(5′)ppp2′OMeAp2′OMeG (FIG., compound 20).The trinucleotide cap analog is produced by the method of Lewdorowicz2007. A mixture of ammonium salt of pApG (compound 19 produced inExample 7), four equivalents of a sodium salt of m⁷GDP-IM (compound 1produced in Example 1), and ZnCl2 in DMF is stirred for 2 days at roomtemperature. The reaction is quenched by addition of water to yieldm⁷G(5′)ppp2′OMeAp2′OMeG (compound 20).

Example 6

4-chlorophenyl((2R,3S,4S,5R)-2-(O-DMT)-4-methoxy-5-(6-(N-methylbenzamido)-9H-purin-9-yl)tetrahydrofuran-3-yl)phosphate (m⁶-benzoyl-2′-OMe-AMP-PhCl, FIG. 7 compound 18). Commerciallyavailable 2′OMe-adenosine compound 4 was diazotized in aqueous aceticacid with nitrous acid to give compound 15 (step i) by the method ofHyde, 2003, J Med Chem, 46:1878-85 (hereby incorporated by reference).Compound 15 was converted to a compound 16 by the method of Miller,2015, J Med Chem, 58:6248-6263 (hereby incorporated by reference) (stepii). The m⁶2′OMe-adenosine product (compound 16) was protected by themethod of Zhu, 2003, Synthetic Communications, 33:1233-43 (herebyincorporated by reference) (step iii). The adenosine compound wasreacted with 1.1 equivalents of TMSCl per hydroxy group together with1.2 equivalents of benzoyl chloride to produce TMS-modified,mono-benzoylated m⁶2′OMe-adenosine. The TMSA groups were removed underaqueous acidic conditions in THF-TFA to give compound 17 (step iii). The5′-hydroxy was reacted with DMT-Cl to form an ether and thephosphorylated adenosine compound 18 was produced as in Example 2 byreaction with 4-chlorophenyl dichlorophosphate as a 3′-O-phosphorylatingagent (FIG. 7, step iv) to produce benzoyl-3′-p-m⁶2′-OMeA (compound 18).

Example 7

Dinucleotide m⁶2′OMeAp2′OMeG (compound 21, FIG. 8). Compound 21 isproduced by combining benzoyl-3′-p-m⁶2′-OMeA compound 18 (Example 7)with protected 2′OMe adenosine compound 9 (Example 3) by the method ofLewdorowicz 2007. First, 3′-p-2′-OMeA compound 18 is mixed with 1equivalent of 2′OMe guanosine compound 9 in anhydrous acetonitrile andthe mixture is dried by evaporation. A solution of2,4,6,-triisopropylbenzenesulfonyl chloride and N-methylimidazole inacetonitrile is added and reacted for 4 hours to produce the protectedm⁶2′OMeAp2′OMeG dinucleotide compound 19 (FIG. 8, step i).

The protective groups of m⁶2′OMeAp2′OMeG dinucleotide intermediatecompound are removed (FIG. 8, step ii) as described in Example 4 toproduce m⁶2′OMeA-2′OMeG dinucleotide compound 20. The 5′-hydroxy groupof the adenosine group is phosphorylated according to the method ofLewdorowicz 2007 (FIG. 8, step iii). Phosphorus trichloride oxide intrimethyl phosphate is cooled to 4° C. and m⁶2′-OMeA-2′-OMeG is addedand stirred at 4° C. for 3 hours. Tetraethylammoniuum bromide (TEAB) isadded to neutralize the mixture to produce the m⁶2′OMeAp2′OMeGdinucleotide 5′-monophosphate (FIG. 8, compound 21).

Example 8

Trinucleotide Cap Analog, m⁷G(5′)ppp m⁶2′OMeAp2′OMeG (compound 22, FIG.9). The trinucleotide cap analog is produced by the method described inExample 5. A mixture of ammonium salt of pApG (compound 21 produced inExample 7), four equivalents of a sodium salt of m⁷GDP-IM (compound 3produced in Example 1), and ZnCl₂ in DMF is stirred for 2 days at roomtemperature. The reaction is quenched by addition of water to yieldm⁷G(5′)pppm⁶2′OMeAp2′OMeG (compound 22).

Example 9

2′-O,4′-C-methylene-linked bicyclic guanine nucleotide (compound 32,FIG. 10). The locked guanine nucleotide was synthesized according to themethod shown in FIG. 10 starting with commercially available((3aS,6aS)-6-(benzyloxy)-2,2-dimethyltetrahydrofuro[2,3-d][1,3]dioxole-5,5-diyl)dimethanol(compound 23) using the method of Koshkin, 2001, J Org Chem, 66:8504-12(hereby incorporated by reference). The diol compound 23 in anhydrouspyridine was cooled in an ice bath and methanesulfonyl chloride (MsCl)is added. The mixture is stirred for 1 hour at room temperature, dilutedwith ethyl ether, and washed with water. The organic layer was dried(Na₂SO₄), concentrated under reduced pressure, co-evaporated withtoluene, and dried in vacuo (FIG. 10, step i) to yield compound 24. Asolution of this product in 80% trifluoroacetic acid was stirred at roomtemperature for one hour. The solvents were removed under pressure andthe residue is dissolved in dichloromethane (DCM) and washed withsaturated NaHCO₃ to yield compound 24.

Compound 24 was co-evaporated with anhydrous pyridine, dissolved inanhydrous pyridine, and treated with Ac₂O overnight. The reactionmixture was quenched by addition of saturated NaHCO₃ and washed withethyl acetate. The organic layers were combined, washed with brine,dried, and concentrated under pressure (FIG. 10, step ii) to produce amixture of two isomers of compound 25.

N,O-Bis(trimethylsilyl)acetamide (BSA) was added to a mixture ofcompound 25 and butyrated guanine in anhydrous acetonitrile. Afterrefluxing for one hour, trimethylsilyl triflate is added and refluxingwas continued further for 4 hours to produce a guanine nucleotidecompound 26 (FIG. 10, step iii). The solution was cooled to roomtemperature, diluted with DCM, and washed with saturated NaHCO₃. Theorganic layer was dried, and concentrated under reduced pressure toobtain modified guanine nucleotide intermediate compound 26.

To a solution of the modified guanine nucleotide compound 26 in1,4-dioxane/water (1:1, v:v) was added 2 M NaOH. After stirring 1 hourat room temperature, the reaction was diluted with saturated NaHCO₃ andextracted with DCM (FIG. 10, step iv) to produce the modified bicycleguanine nucleotide. The organic layers were dried and concentrated toobtain the bicyclic product compound 27.

Compound 27 was reacted with sodium benzoate in anhydrous DMF andstirred for 5 hours at 100° C. (FIG. 14, step v). The mixture containingthe 5′O-protected compound 28 was cooled, filtered, and suspended inethyl acetate, washed with water, and dried.

H₂O and 2 M NaOH are added to a solution of compound 28 in 1,4-dioxane.The reaction mixture was refluxed for 24 hours, cooled to roomtemperature, and neutralized with acetic acid (FIG. 10, step vi) toproduce compound 29 having a free 5′OH. Saturated NaHCO₃ was added, andthe mixture was washed with DCM. Organic layers were combined, dried(Na₂SO₄), and concentrated under reduced pressure.

To a solution compound 29 in methanol was added 20% Pd(OH)₂/C, andHCO₂H. After refluxing the mixture for 10 min, the catalyst was filteredoff and washed with methanol (FIG. 14, step vii). The combined filtrateswere concentrated to obtain compound 30 with free 3′ and 5′ OH groups.

The 5′ OH group of compound 30 was blocked as a DMTr ether according tothe method of WO 99/14266 by preparing an anhydrous pyridine solution ofthe nucleotide, adding an excess of 4,4′-dimethoxytrityl chloride,stirring at room temperature for 2 hours, quenching the reaction withice cold water, and extracting the product with DCM (FIG. 10, stepviii). The combined organic phases were washed NaHCO₃-saturated water,brine, and dried Na₂SO₄ to give compound 31.

The 3′-OH group of the nucleotide 31 was blocked by an acyl groupaccording to the method of WO 2009/124238 (hereby incorporated byreference). The 3′ hydroxy group compound 31 was acylated with alkoylchloride, triethylamine in DCM, followed by removal of the 5′O-DMTrgroup with hexafluoroisopropanol or aqueous acid to produce the lockedguanyl nucleotide, compound 32 (FIG. 10, step viii).

Example 10

Dinucleotide m⁶2′OMeAp-locked-2′OMeG (compound 35, FIG. 11). Thedinucleotide was produced by combining locked guanyl nucleotide,compound 32 (Example 9) with benzoylated 3′-p-m⁶2′-OMeA compound 18(Example 6) by the method of Lewdorowicz 2007. Locked guanyl compound 32was mixed with 1 equivalent of benzoylated 3′-p-m⁶2′-OMeA compound 18 inanhydrous acetonitrile and the mixture was dried by evaporation. Asolution of 2,4,6,-triisopropylbenzenesulfonyl chloride andN-methylimidazole in acetonitrile was added and reacted for 4 hours toproduce the protected m⁶2′-OMeAp-locked-2′-OMeG dinucleotide compound 33(FIG. 11, step i).

The protective groups of dinucleotide compound 33 were removed (FIG. 11,step ii) as described in Example 4 to produce m⁶2′OMeA-locked-2′-OMeGdinucleotide compound 34. The 5′-hydroxy group of the adenosine groupwas phosphorylated according to the method of Lewdorowicz 2007 (FIG. 11,step iii). Phosphorus trichloride oxide in trimethyl phosphate wascooled to 4° C. and m⁶2′OMeA-2′OMeG was added and stirred at 4° C. for 3hours. Tetraethylammoniuum bromide (TEAB) was added to neutralize themixture to produce the m⁶2′-OMeAp-locked-2′-OMeG dinucleotide5′-monophosphate (FIG. 11, compound 35).

Example 11

Trinucleotide cap analog, m⁷G(5′)pppm⁶2′OMeAp-locked-2′-OMeG (compound36, FIG. 12). The trinucleotide cap analog is produced by the methoddescribed in Example 5. A mixture of ammonium salt ofm⁶2′-OMeAp-locked-2′-OMeG dinucleotide 5′-monophosphate (compound 35produced in Example 10), four equivalents of a sodium salt of m⁷GDP-IM(compound 3 produced in Example 1), and ZnCl₂ in DMF is stirred for 2days at room temperature. The reaction is quenched by addition of waterto yield m⁷G(5′)pppm⁶2′-OMeAp-locked-2′-OMeG (compound 36).

Example 12

(R)-3-hydroxy-2-((R)-1-(2-isobutyramido-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-methoxyethoxy)propylisobutyrate (2′OMe-seco-3′-O-isobutyryl,N²-isobutyrylguanosine; FIG. 13,compound 43). The 5′ OH group of N²-isobutyrylguanosine compound 37 wasblocked by as a DMTr ether according to the method of WO 99/14266 bypreparing a anhydrous pyridine solution of the nucleotide, adding anexcess of 4,4′-dimethoxytrityl chloride, stirring at room temperaturefor 2 hours, quenching the reaction with ice cold water, and extractingthe product (compound 38) with DCM (FIG. 13, step i). The combinedorganic phases were washed with NaHCO₃-saturated water, brine, and driedNa₂SO₄.

Guanosine compound 38 was converted to an “unlocked” form of compound 39by the method of Landkjaer, 2009, Biorg Med Chem, 17:5420-25 (herebyincorporated by reference). The DMTr guanosine compound 38 was dissolvedin a stirred mixture of dioxane and water. To this mixture was addedNaIO₄ dissolved in water, stirred for one hour, and further dioxane isadded. The suspension was filtered and the filter cake was washed withdioxane. The filtrates were combined and sodium borohydride was addedand the mixture stirred for 30 minutes (FIG. 17, step ii). The mixturewas neutralized by addition of pyridine:acetic acid buffer. Afterevaporation, DCM is added and the mixture was washed with saturatedaqueous NaHCO₃. The organic phase was separated and evaporated todryness under reduced pressure, to yield 5′O-DMT-2′,3′-secoguanine.

2′-O-benzoyl-5′-O-DMT-2′,3′-secoguanine compound 39 was prepared from5′O-DMT-2′,3′-secoguanine by the method of Landkjaer 2009. Thenucleotide was co-evaporated with anhydrous toluene and dried for 12hours in vacuo. The residue was dissolved at room temperature inanhydrous mixture of DCM with pyridine and cooled to −78° C. Benzoylchloride was added over 15 minutes with stirring for 1 hour at −78° C.The mixture was warmed to room temperature, and ethanol was added andthe mixture was washed with saturated aqueous NaHCO₃ and the separatedaqueous phase was back-extracted with DCE. The organic phases werecombined and evaporated to dryness to yield the 2′-O-benzoylatedsecoguanine compound 39 (FIG. 13, step ii).

The 3′-OH group of the the 2′-O-benzoylated secoguanine was protected byTBDMSCl according to the method of Perlikova 2014, ChemBioChem,15:146-156 (hereby incorporated by reference) (FIG. 13, step iii) toyield compound 40.

The 2′-O-benzoyl group compound 40 was removed by the method of Nishino,1985, Tetrahedron, 41:5503-06 (hereby incorporated by reference) using asuspension of sodium methoxide in THF for 1 hour at room temperature(FIG. 13, step iv). The reaction was quenched by neutralization to yieldthe free 2′-OH group of compound 41.

The 2′-OH group of compound 41 was methylated by reaction with NaH andmethyl iodide in THF at 0° C. (step v) to yield compound 42. The silylgroup was removed from the 3′-OH group with nBu₄NF by the method ofPerlikova 2014 and the 3′-OH group was butyrlated (step v) to producethe secoguanine compound 43 after removal of the DMTr protecting groupwith acid (CF₃CO₂H, step vi).

Example 13

((2R,3S,4S,5R)-3-((((S)-2-((R)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-methoxyethoxy)-3-hydroxypropoxy)(hydroxy)phosphoryl)oxy)-4-methoxy-5-(6-(methylamino)-9H-purin-9-yl)tetrahydrofuran-2-yl)methylhydrogen phosphate (p-2′-OMe-m⁶Ap-seco-2′-OMeG, FIG. 14, compound 46).Protected 2′OMeAp2′OMeG dinucleotide, compound 44 (FIG. 14) was producedby combining 3′-p-2′-OMeA compound 18 (Example 6) with protected 2′-OMesecoguanosine compound 43 (Example 12) by the method of Lewdorowicz2007. First, 3′-p-2′-OMeA compound 18 was mixed with an equivalent of2′OMe guanosine compound 43 in anhydrous acetonitrile and the mixturewas dried by evaporation. A solution of2,4,6,-triisopropylbenzenesulfonyl chloride and N-methylimidazole inacetonitrile was added and the mixture was reacted for 4 hours toproduce compound 44 (FIG. 14, step i).

The protective groups of compound 44 were removed (step ii, usingreactions described in Example 4, FIG. 5, step i), to produce a2′-OMeA-2′-OMeG dinucleotide compound 45. The 5′-hydroxy group of theadenosine group was phosphorylated according to the method ofLewdorowicz 2007 (FIG. 14, step iii). Phosphorus trichloride oxide intrimethyl phosphate was cooled to 4° C. and the 5′-O-guanine-adeninedinucleotide-3′-O compound 45 was added and stirred at 4° C. for 3hours. Tetraethylammoniuum bromide (TEAB) was added to neutralize themixture to produce 2′-OMe-m⁶Ap-seco-2′-OMeG 5′-monophosphate, compound46.

Example 14

Trinucleotide cap analog, m⁷G(5′)pppm⁶2′-OMeAp-seco-2′-OMeG (compound54, FIG. 19). The trinucleotide cap analog is produced by the methoddescribed in Example 8. A mixture of ammonium salt of2′-OMe-m⁶Ap-seco-2′-OMeG 5′-monophosphate, compound 53 (produced inExample 16), four equivalents of a sodium salt of m⁷GDP-IM (compound 1produced in Example 1), and ZnCl2 in DMF is stirred for 2 days at roomtemperature. The reaction is quenched by addition of water to yieldm⁷G(5′)pppm⁶2′OMeAp-seco-2′OMeG (compound 54).

Example 15

(2R,3S,4S,5R)-2-(hydroxymethyl)-5-(2-isobutyramido-6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-3,4-diylbis(2-methylpropanoate(2′-O-isobutyryl-3′O-isobutyryl,N²-isobutyrylguanosine, FIG. 16,compound 50) is synthesized from commercially available guanosine(compound 48) by the method of Wolf, 2008, Org Biomol Chem, 6:899-907(hereby incorporated by reference). First, guanosine is isobutyrated atthe N² position and crystallized from water to giveN²-isobutyrylguanosine, and the 5′-hydroxy group is protected with aDMTr group (FIG. 16, step i) according to the method of WO 99/14266 toyield compound 49. Second, 2′- and 3′ hydroxy groups are subject toisobutyrylation, and the DMTr group is removed by treatment with 5%trichloroacteic acid to produce2′-O-isobutyryl,3′-O-isobutyryl,N²-isobutyrylguanosine, compound 50(FIG. 16, step ii).

Example 16

((2R,3S,4S,5R)-3-(((((2R,3R,4S,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methoxy)oxidophosphoryl)oxy)-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl)methylhydrogen phosphate (p-2′-OMe-ApG, FIG. 18, compound 53). To synthesizep-2′-OMe-ApG, compound 6 (5′O-DMT-2′O-Me-N⁶benzoyl-AMP-PhCl, Example 2)is combined with isobutyrated guanosine compound 50 (Example 15) by themethod of Lewdorowicz 2007. Compound 6 is mixed with an equivalent ofisobutyrated guanosine compound 50 in anhydrous acetonitrile. Themixture is dried by evaporation. A solution of2,4,6,-triisopropylbenzenesulfonyl chloride and N-methylimidazole inacetonitrile is added and the mixture is reacted for 4 hours to producethe protected 2′-OMe-ApG dinucleotide compound 51 (FIG. 17, step i).

The protective groups of 2′-OMeApG dinucleotide compound 51 are removedusing known reactions, e.g., by a method selected from Lewdorowicz 2007;Huss, 1988, J Org Chem, 53:499-506; Zhou, 1986, Tetrahedron, 42:4149-56;Reese, 1986, Tetrahedron Letters, 27:2291-94; Abramova, 2008, Biorg MedChem, 16:9127-32; Abramova, 2013, Beilstein J Org Chem, 9:2898-909;Hashmi, 1994, Nucleotides & Nucleotides, 13:1059-67; Hsu, 1985,Nucleotides & Nucleotides, 4:377-89; Puech, 1988, J Med Chem,31:1897-907 (hereby incorporated by reference) (FIG. 18, step i) toproduce 2′-OMe-ApG dinucleotide (compound 52). The 5′-hydroxy group ofcompound 52 is phosphorylated according to the method of Lewdorowicz2007 (step ii). Phosphorus trichloride oxide in trimethyl phosphate iscooled to 4° C. and the 5′-O-guanine-adenine dinucleotide-3′-Ointermediate is added and stirred at 4° C. for 3 hours.Tetraethylammoniuum bromide (TEAB) is added to neutralize the mixture toproduce p-2′-OMe-ApG dinucleotide (FIG. 18, compound 53).

Example 17

Trinucleotide cap analog, m⁷G(5′)ppp-2′OMeApG (compound 54 of FIG. 19).The trinucleotide cap analog is produced by the method of Lewdorowicz2007. A mixture of ammonium salt of pApG (compound 53 produced inExample 18), four equivalents of a sodium salt of m⁷GDP-IM (compound 3produced in Example 1), and ZnCl₂ in DMF is stirred for 2 days at roomtemperature. The reaction is quenched by addition of water to yieldm⁷G(5′)ppp-2′OMeApG (compound 54).

Example 18

In Vitro Transcription Reaction:

For ARCA and ARC CAP1 mRNAs, in vitro transcription was performed usingthe standard protocol (see Table, below). All of components were mixed,and T7 RNA polymerase (E2040 from NEB) was added in the reactionmixture. The transcription reaction was incubated for 2 hrs at 37 C.After 2 hrs of reaction time, DNASEI (NEB) and buffer were added to thetranscription reaction and incubated for 15 mins at 37 C. The crude ofreaction mix was purified using RNA purification kit (Macherey-Nagel).

Transcription Component Amount to Component Type Name add (ul) WaterWater up to 200 uL rNTPs rATP (100 mM) 10 rCTP (100 mM) 10 rN1MPU (100mM) 10 rGTP (100 mM) 10 ARCA* or 10 ARC CAP1** (100 mM) 10X rxn buffer10x rxn buffer 20 Template Linear Plasmid 10 ug Enzymes RNase Inhibitor5 (40 U/uL) Inorganic 4 Pyrophosphatase (0.1 U/uL) T7 Mix 8 *ARCA,3′-OMe-m⁷G(5′)p₃G (Trilink) **ARC CAP 1, m⁷G(5′)p₃AmpG

For Vaccinia mRNA, in vitro transcription was performed using thestandard protocol without ARCA or ARC CAP1. All of components weremixed, and T7 RNA polymerase (E2040 from NEB) was added in the reactionmixture. The transcription reaction was incubated for 2 hrs at 37 C.After 2 hrs of reaction time, DNASEI (NEB) and buffer were added to thetranscription reaction and incubated for 15 mins at 37 C. The crude ofreaction mix was purified using RNA purification kit (Macherey-Nagel).The RNA was denatured at 65° C. for 5 min and then snap chilled torelieve any secondary conformations. For the total 1 mL cappingreaction, 1 mg denatured RNA in 700 μL of nuclease-free water was usedalong with 100 μL 1 (10×) capping buffer, 50 μL (10 mM) GTP, 50 μL (4mM) SAM, 50 μL of (10 units/μL) Vaccinia capping enzyme, and 50 μL ofmRNAcap2′-O-methyltransferase at (50 units/μL) were combined andincubated at 37° C. for 1 h. The mixture capped mRNA was purified usingRNA purification kit (Macherey-Nagel).

m⁷G(5′)p₃-RNA were delivered 0.3 mg/kg i.v. into 12-16 weeks old malemice. Blood samples were collected at 6 hours post dose, and plasma wasisolated. Protein expression was performed using ELISA (e.bioscience).Results are shown in FIG. 16.

The results show that the efficiency of transcription usingtrinucleotide analog ARC CAP1 is substantially improved compared todinucleotide ARCA. This is because the amount of protein expression forARC CAP1 is greater than ARCA, and because vaccinia-mediated cappingproduces m⁷G(5′)p₃-RNA that results in comparable protein expressioncompared to ARC CAP1. ARC CAP1-RNA is just as efficient translated asenzymatically capped RNA.

Although the present disclosure is described with respect to certainembodiments and examples, various modifications may be made withoutdeparting from the spirit and scope of the invention.

What is claimed is as follows:
 1. A compound of formulam⁷G(5′)p₃(5′)N₁pN₂, wherein m⁷G is a ribonucleotide consisting ofN⁷-methylguanine and a ribose or a modified ribose, wherein one or bothof the 2′ or 3′ carbons of the modified ribose has a fluoro or a C1-C6alkoxy substituent; (5′)p₃(5′) is a 5′ to 5′ triphosphate linkage,wherein the triphosphate linkage may be substituted with one or morephosphorothioate groups; N₁ is a ribonucleotide comprising a seco (UNA)ribose optionally substituted at the 2′ or 3′ carbons with one or morefluoro or C1-C6 alkoxy substituents, and a base selected from the groupconsisting of adenine, uridine, guanine, cytosine, N⁶-methyladenine,N¹-methyladenine, pseudouracil, N¹-methylpseudouracil, 5-iodouracil,4-thiouracil, 2-thiouracil, 5-methyluracil, pseudoisocytosine,5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N⁴-methylcytosine,5-hydroxymethylcytosine, hypoxanthine, N¹-methylguanine,O⁶-methylguanine, N²-methylguanine (m²G), N²,N²-dimethylguanine(m^(2,2)G), N²,N⁷-dimethylguanine (m^(2,7)G), and isoguanine; and N₂ isa ribonucleotide consisting of (i) a base selected from the groupconsisting of adenine, uridine, guanine, cytosine, N⁶-methyladenine,N¹-methyladenine, pseudouruacil, N¹-methylpseudouracil, 5-iodouracil,4-thiouracil, 2-thiouracil, 5-methyluracil, pseudoisocytosine,5-methoxycytosine, 2-thiocytosine, 5-hydroxycytosine, N⁴-methylcytosine,5-hydroxymethylcytosine, hypoxanthine, N¹-methylguanine,O⁶-methylguanine, N²-methylguanine (m²G), N²,N²-dimethylguanine(m^(2,2)G), N²,N⁷-dimethylguanine (m^(2,7)G), and isoguanine; and (ii) aribose moiety comprising a ribose or a modified ribose, wherein one orboth of the 2′ or 3′ carbons of the modified ribose has a fluoro or aC1-C6 alkoxy substituent; wherein the m⁷G ribonucleotide is linked atits 5′-OH to the triphosphate bridge, the triphosphate bridge is linkedto a 5′-OH of the N₁ ribonucleotide, the N₁ nucleotide is linked via its3′-OH to a phosphate, p, and the phosphate is linked to a 5′-OH of theN₂ ribonucleotide; or a salt or solvated form thereof.
 2. The compoundof claim 1, wherein the base of N₁ is adenine, uridine, guanine, orcytosine.
 3. The compound of claim 2, wherein the base of N₁ is adenine.4. The compound of claim 2, wherein one or both of the 2′ or 3′ carbonsof the seco (UNA) ribose of N₁ has a fluoro or a C1-C6 alkoxysubstituent.
 5. The compound of claim 2, wherein the 2′ carbon of theseco (UNA) ribose of N₁ has a fluoro or a C1-C6 alkoxy substituent. 6.The compound of claim 2, wherein the 2′ carbon of the seco (UNA) riboseof N₁ has a C1-C6 alkoxy substituent.
 7. The compound of claim 2,wherein the 2′ carbon of the seco (UNA) ribose of N₁ has a methoxysubstituent.
 8. The compound of claim 1, wherein the base of N₂ isselected from the group consisting of guanine, N₁-methylguanine,O⁶-methylguanine, m²G, m^(2,2)G, m^(2,7)G, and isoguanine.
 9. Thecompound of claim 8, wherein the base of N₂ is guanine,N₁-methylguanine, O⁶-methylguanine, or isoguanine.
 10. The compound ofclaim 8, wherein the base of N₂ is guanine.
 11. The compound of claim 1,wherein the 2′ carbon of at least one of m⁷G, N₁, or N₂ ribonucleotideis substituted by a C1-C6-alkoxy.
 12. The compound of claim 1, whereinat least one ribose of the N₁ or N₂ ribonucleotide is substituted by a2′-O-methyl.
 13. The compound of claim 1, wherein the triphosphatebridge consists of 1, 2, or 3 phosphorothioate groups.
 14. The compoundof claim 1, wherein the compound is m⁷G(5′)p₃-seco-2′-OMeA-G, whereinseco-2′-OMeA is 2′-O-methyladenosine-seco(UNA)ribose and G is guanosine.15. The compound of claim 1, wherein the compound increases theefficiency of m⁷G(5′)p₃-RNA produced by in vitro transcription comparedto 3′-OMe-m⁷G(5′)p₃G.
 16. The compound of claim 15, wherein in vitrotranscription is mediated by T7 RNA polymerase or T6 RNA polymerase.